Following the meeting today I made a couple of quick mockups for how I see the installer section of the combined launcher/updater/installer working.
Firstly the launcher would be a standalone, cross-platform program. It would not live in the FS2 folder but instead would live in one of its own (if you want you could install FS2 in a subfolder below it of course). The launcher would either be installed as part of a TC download or on its own. Once run the launcher would then look at its ini file. The ini file would contain a list of folders on the users harddrive to search for FS2_Open games.
The Launcher then checks those folders looking for mod.ini files (we can also make it look for launcher6.ini files for compatibility reasons if we want). It uses those to populate its internal list of mods and TCs. If the user has something installed it goes to the run game tab allowing the user to set up the game.
If the user has nothing installed or the user then clicks on the Install tab, the launcher goes online and checks the website the current installer does (or a new one). It finds the master list of mods and TCs available for download. It then contacts each of them and sees what they have available. It then presents the user with something like this screen.

The master list is a text file which states the name of the mod or TC and the URL of a text file describing where the download for it is located (allowing each mod to remain in charge of updates, etc themselves). Each mod then provides its own text file at that location which has certain data.
1) The version number of the mod
2) The name of any mods or games it requires (so Operations would state TBP (and maybe Zathras) here)
3) The URLs for the downloads plus CRCs, etc for them.
4) CRCs for old files which are no longer part of the mod can be included as an option.

When the user clicks to download the game checks if there are any requirements. It then checks if the required game is already installed (i.e in the internal list it compiled earlier. If the game is present it then checks if the game is up to date (we could supply minimum version numbers if we wanted to so that you don't need to be 100% up to date, merely up to date enough for the mod).
It does this by checking section 2) and then contacting the URL the master list gave for that mod or TC. So in the case of Operations it would check the master list, find the text file for TBP and then check if the CRCs of the .vp files for TBP matched the ones of the files on the HD.
If there are no issues, it starts to download. Otherwise....

If we handled this all correctly we could probably wipe out a huge portion of our support work cause checking that mods are installed properly could all be handled by the launcher. Best of all, none of this should get in the way of a manual install. We'd add a settings tab and simply allow users to manually tell the installer where they have installed mods by hand.
Furthermore instead of maintaining a central .ini file for the launcher by making it save the set up in the folder belonging to the game (or even mod) we allow the user to choose to use the same launcher to run 3.6.11 for WCS, 3.7 for Diaspora and 3.8 for anything else with different settings.